https://github.com/aehrc/pathling

Tools that make it easier to use FHIR and clinical terminology within data analytics, built on Apache Spark.
https://github.com/aehrc/pathling

analytics fhir spark standards terminology

Last synced: about 1 month ago
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Tools that make it easier to use FHIR and clinical terminology within data analytics, built on Apache Spark.

Host: GitHub
URL: https://github.com/aehrc/pathling
Owner: aehrc
License: apache-2.0
Created: 2020-03-23T05:22:00.000Z (about 6 years ago)
Default Branch: main
Last Pushed: 2026-02-13T10:03:02.000Z (4 months ago)
Last Synced: 2026-02-13T10:16:07.896Z (4 months ago)
Topics: analytics, fhir, spark, standards, terminology
Language: Java
Homepage: https://pathling.csiro.au
Size: 206 MB
Stars: 118
Watchers: 11
Forks: 19
Open Issues: 88
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff

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[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=aehrc_pathling&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=aehrc_pathling)

Pathling is a set of tools that make it easier to

use [FHIR®](https://hl7.org/fhir) and clinical terminology within health

data analytics. It is built on [Apache Spark](https://spark.apache.org), and

it implements the [SQL on FHIR](https://sql-on-fhir.org) view specification and

the [Bulk Data Access](https://hl7.org/fhir/uv/bulkdata/STU2/) implementation

guide.

[**Read the documentation →**](https://pathling.csiro.au/docs)

## What can it do?

### Query and transformation of FHIR data

[FHIR R4](https://hl7.org/fhir) is the dominant standard for exchanging health

data. It comes in both [JSON](https://hl7.org/fhir/json.html)

or [XML](https://hl7.org/fhir/xml.html) formats, and can contain over 140

different types of resources, such

as [Patient](https://hl7.org/fhir/patient.html),

[Observation](https://hl7.org/fhir/observation.html),

[Condition](https://hl7.org/fhir/condition.html),

[Procedure](https://hl7.org/fhir/procedure.html), and many more.

Pathling is capable of reading all the different types of FHIR resources into a

format suitable for data analysis tasks. This makes the following things

possible:

- Creating SQL-friendly views from FHIR data

- Transforming data into other formats, such as CSV

  or [Parquet](https://parquet.apache.org/)

- Performing terminology queries against coded fields within the FHIR data

See [Data in and out](https://pathling.csiro.au/docs/libraries/io) and

[Running queries](https://pathling.csiro.au/docs/libraries/running-queries) for

more information.

### Terminology queries

Health data often contains codes from systems such

as [SNOMED CT](https://www.snomed.org/snomed-ct/five-step-briefing), [LOINC](https://loinc.org/)

or [ICD](https://www.who.int/standards/classifications/classification-of-diseases).

These codes contain a great deal of information about diagnoses, procedures,

observations and many other aspects of a patient's clinical record.

It is common to group these codes based upon their properties, relationships to

other codes, or membership within a pre-defined set. Pathling can automate the

task of calling out to

a [FHIR terminology server](https://hl7.org/fhir/terminology-service.html) to

ask questions about the codes within your data.

Examples of the types of questions that can be answered include:

- Is this SNOMED CT procedure code a type of endoscopy?

- Does this LOINC test result code have an analyte of bilirubin?

- Is this ICD-10 code within the pre-defined list of codes within my cohort

  definition?

See [Terminology functions](https://pathling.csiro.au/docs/libraries/terminology)

for more information.

### Server

Pathling Server is a FHIR R4 analytics server that exposes a range of

functionality for use by applications and implements:

- **SQL on FHIR**:

  [Run](https://pathling.csiro.au/docs/server/operations/view-run) view

  definitions to

  preview tabular projections of FHIR data,

  then [export](https://pathling.csiro.au/docs/server/operations/view-export) to

  NDJSON, CSV, or Parquet

- **Bulk Data Access

  **: [Export data](https://pathling.csiro.au/docs/server/operations/export) at

  system,

  patient, or group level using the FHIR Bulk Data Access specification

- **Bulk Import

  **: [Import data](https://pathling.csiro.au/docs/server/operations/import)

  from NDJSON,

  Parquet, or Delta Lake sources,

  or [sync with another FHIR server](https://pathling.csiro.au/docs/server/deployment/synchronization)

  that supports bulk export

- **[Bulk Submit](https://pathling.csiro.au/docs/server/operations/bulk-submit)

  **: An experimental

  implementation of the new Bulk Submit proposal

- **[FHIRPath Search](https://pathling.csiro.au/docs/server/operations/search)

  **: Query resources using

  FHIRPath expressions

- **[CRUD Operations](https://pathling.csiro.au/docs/server/operations/crud)**:

  Create, read, update, and

  delete resources

The server is distributed as a Docker image. It

supports [authentication](https://pathling.csiro.au/docs/server/authorization)

and also can be scaled

over a cluster

on [Kubernetes](https://pathling.csiro.au/docs/server/deployment/kubernetes) or

other

Apache Spark clustering solutions.

See [Server](https://pathling.csiro.au/docs/server) for installation and

configuration details.

## Artifact signing

Published Maven artifacts and Helm charts are signed with the following GPG key:

- **Key ID**: `ED48678D`

- **Fingerprint**: `F814 751C 64B5 F5E7 08A8 C73F C3C6 291F ED48 678D`

- **User ID**: `Pathling Developers `

The public key is available

on [keys.openpgp.org](https://keys.openpgp.org/search?q=F814751C64B5F5E708A8C73FC3C6291FED48678D).

## Licensing and attribution

Pathling is copyright © 2018-2025, Commonwealth Scientific and Industrial

Research Organisation

(CSIRO) ABN 41 687 119 230. Licensed under

the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).

This means that you are free to use, modify and redistribute the software as

you wish, even for commercial purposes.

If you use this software in your research, please consider citing our paper,

[Pathling: analytics on FHIR](https://doi.org/10.1186/s13326-022-00277-1).

**Pathling is experimental software, use it at your own risk!** You can get a

full description of the current set of known issues

[here](https://github.com/aehrc/pathling/issues).

ecosyste.ms

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